title: Administration of multivalent influenza virus recombinant hemagglutinin vaccine in combination-adjuvant elicits broad reactivity beyond the vaccine components

city: Irvine

middle: Huw

last: Davies

state: CA

address: 812 Medical Plaza Drive, Med Surge II, Rm 376

department: Physiology & Biophysics

institute: UC Irvine

summary: Combining variant antigens into a multivalent vaccine is a traditional approach used to provide broad coverage against antigenically variable pathogens, such as polio, human papilloma and influenza viruses. However, strategies for increasing the breadth of antibody coverage beyond the vaccine are not well understood, but may provide more anticipatory protection. Influenza virus hemagglutinin (HA) is a prototypic variant antigen. Vaccines that induce HA-specific neutralizing antibodies lose efficacy as amino acid substitutions accumulate in neutralizing epitopes during influenza virus evolution. Here we studied the effect of a potent combination adjuvant (CpG/MPLA/squalene-in-water emulsion) on the breadth and maturation of the antibody response to a representative variant of HA subtypes H1, H5 and H7. Using HA protein microarrays and antigen-specific B cell labelling, we show when administered individually, each HA elicits a cross-reactive antibody profile for multiple variants within the same subtype and other closely-related subtypes (homosubtypic and heterosubtypic cross-reactivity, respectively). Despite a capacity for each subtype to induce heterosubtypic cross-reactivity, broader coverage was elicited by simply combining the subtypes into a multivalent vaccine. Importantly, multiplexing did not compromise antibody avidity or affinity maturation to the individual HA constituents. The use of adjuvants to increase the breadth of antibody coverage beyond the vaccine antigens may help future-proof vaccines against newly-emerging variants.

platform_organism:
Influenza A virus
Influenza B virus

overall_design: A combination adjuvant comprising MPLA, CpG ODN1018, and AddaVax™ (a squalene-in-water emulsion) was used to formulate recombinant trimers of influenza virus hemagglutinins H1, H5 or H7 into monovalent or trivalent vaccines, which were then evaluated for the breadth of antibody response induced after single dose or prime-boost administration into C57Bl/6 mice. The breadth of response was measured using a custom protein microarray comprising multiple HA variants spanning HA subtypes H1 to H18, represented as full-length (HA0) proteins and HA1 domains.

first: Jenny

middle: E

last: Hernandez-Davies

first: Jiin

last: Felgner

first: Shirin

last: Strohmeier

first: Egest

last: Pone

first: Aarti

last: Jain

first: Sharon

last: Jan

first: Rie

last: Nakajima

first: Algimantas

last: Jasinskas

first: Erwin

last: Strahsburger

first: Florian

last: Krammer

first: Philip

first: D


title: Transcriptional-Regulatory Convergence Across Functional MDD Risk Variants Identified by Massively Parallel Reporter Assays

status: Public on Jun 30 2021

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: 660 S Euclid Ave, Campus Box 8232

department: Genetics

country: USA

institute: Washington University in St. Louis

type: Expression profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Escherichia coli
Mus musculus

platform_organism:
Escherichia coli
Mus musculus

overall_design:
Refer to individual Series
Grants:
1. 5F30MH116654 - Bernard Mulvey - Identification and characterization of common, noncoding regulatory variants associated with Major Depressive Disorder - NIMH

2. 1R01MH116999 - Joseph Dougherty - Highly parallel analysis of 5' and 3' UTR variants in Autism Spectrum Disorders - NIMH

3. 571009 - Joseph Dougherty - Simons Foundation


title: Amnion signals are essential for mesoderm formation in primates

city: Solna

first: Alexander

last: Goedel

address: Solnavägen 9

department: Department of Cell and Molecular Biology (CMB)

country: Sweden

institute: Karolinska Institutet

summary: Embryonic development is largely conserved among mammals. However, certain genes show divergent functions. By generating a transcriptional atlas containing >30,000 cells from post-implantation non-human primate embryos, we uncover that ISL1, a gene with a well-established role in cardiogenesis, controls a gene regulatory network in primate amnion. CRISPR/Cas9-targeting of ISL1 results in non-human primate embryos which do not yield viable offspring, demonstrating that ISL1 is critically required in primate embryogenesis. On a cellular level, mutant ISL1 embryos display a failure in mesoderm formation due to reduced BMP4 signaling from the amnion. Via loss of function and rescue studies in human embryonic stem cells we confirm a similar role of ISL1 in human in vitro derived amnion. This study highlights the importance of the amnion as a signaling center during primate mesoderm formation and demonstrates the potential of in vitro primate model systems to dissect the genetics of early human embryonic development.

overall_design: Single cell gene expression profiling (mRNA) of in vitro cultured wildtype and ISL1 hypomorphic mutant cynomologus monkey embryos at Day 10, Day 12 and Day 14. WT-batch 1: D10 2 embryos, D12 1 embryo, D14 2 embyos; WT-batch 2: D10 3 embryos, D12 2 embryos, D14 2 embryos; ISL1-mutant batch-1: D10 3 embryos, D12 3 embryos, D14 3 embryos; ISL1-mutant batch-2: D12 1 embryo, D14 1 embryo

first: Ran

last: Yang

first: Kenneth

middle: R

last: Chien


title: The BMP antagonist Gremlin1 contributes to the development of cortical excitatory neurons, motor balance and fear responses

city: Adelaide

first: Susan

last: Woods

state: Select State

address: Level 5 South, SAHMRI building, North Terrace

department: School of Medicine

country: Australia

institute: The University of Adelaide

summary: Introduction: Bone morphogenetic protein (BMP) signaling is required for early forebrain development, however the role of this signalling pathway in later cortical patterning awaits careful mechanistic investigation. How the endogenous modulators of BMP signaling regulate the structural and functional maturation of the developing brain remains unclear.  Aim: To investigate the expression and function of the BMP antagonist Gremlin1 (Grem1) in the developing mouse brain.  Methods: The role of Grem1 in neuronal differentiation was assessed using neural stem cell (NSC) and progenitor cell culture ex vivo. Lineage tracing of Grem1 expressing cells in the fetal brain was examined by administration of tamoxifen to pregnant Grem1creERT; Rosa26LSLTdtomato mice at 13.5 days post coitum (dpc), followed by collection of embryos later in gestation. In addition, at 14.5 dpc cells from the dorsal telencephalon were FACS sorted into Grem1 positive and negative cells and bulk mRNA seq analysis of differentially expressed transcripts between the two cell populations was performed. We also generated Emx1-cre mediated Grem1 conditional knockout mice (Emx1-Cre;Grem1flox/flox, Grem1Emx1 cKO, in which the Grem1 gene was deleted specifically in the dorsal telencephalon and assessed brain histology and mouse behavior.   Results: Grem1 positive cells were located in the lower cortical plate and subplate at E14.5 and migrated towards the lateral ventricle. Grem1 cells expressed immature neuron markers, self-renewed and gave rise to layer Ⅴ and Ⅵ excitatory glutamatergic neurons. GREM1 expression also identifies a similar population of excitatory neurons in the developing human brain. Recombinant Grem1 treatment induced neural differentiation of NSCs in vitro, whilst Grem1Emx1 cKO animals had reduced thickness of the cortex, especially layers Ⅴ and Ⅵ. Behavioural tests revealed Grem1Emx1 cKO mice have impaired motor balance and fear sensitivity compared to littermate controls.  Conclusion: Grem1 expression marks an early neuronal progenitor that gives rise to excitatory neurons in the embryonic mouse brain. This BMP antagonist functions to promote neural progenitor proliferation and neuronal differentiation.

overall_design: Grem1 traced mouse brains were harvested at 24 hours post tamoxifen induction. Grem1 positive and negative population were separated via FACS. RNA seq were then performed on these two populations. Differential gene expression of Grem 1 positive vs Grem1 negative populations were then performed, and subsequently network analyses on Grem1 positive population to reveal the distinct biological activity.

first: Mari

last: Ichinose

first: Nobumi

last: Suzuki

first: Martin

last: Lewis

first: Ryota

last: Ando

first: Atushi

last: Enomoto

first: Simon

last: Koblar

middle: L

first: Paul

last: Thomas

first: Daniel

last: Worthley


title: Effect of H2O2 and Collagen tripeptide (CTP) on endothelial cells and smooth muscle cells in cell culture

status: Public on Jun 29 2021

city: Kahoku-gun

first: Yasuo

last: Yoshitomi

state: Ishikawa

address: 1-1 Daigaku, Uchinada-machi

department: Biochemistry

country: Japan

institute: Kanazawa Medical University

summary: Analysis of gene expression in primary cultured human aortic endothelial cells (HAECs) and primary cultured human aortic smooth muscle cells (SMCs) with or without H2O2 or Collagen tripeptide (CTP)

overall_design: Gene expression profiling of human heart endothelial cells and smooth muscle cells with or without H2O2 and Collagen tripeptide (CTP) treatment in vitro.

first: H

last: Yonekura

first: Y

last: Ishigaki

last: Nakamura


title: Combining Genome-wide Gene Expression Analysis (RNA-seq) and Gene Editing Platform (CRISPR-Cas9) to Uncover the Selectively Pro-oxidant Activity of Aurone Compound against Candida albicans

city: Murfreesboro

first: Fatmah

last: Alqahtani

state: TN

address: 1301 East Main Street

department: Biology

institute: Middle Tennessee State University

summary: The antifungal activity of aurones SH1009 and SH9051 against Candida albicans was investigated. A whole-genome transcriptional analysis post aurone SH1009 and SH9051 treatments on the C. albicans SC5314 strain was performed using RNA-seq technique.

overall_design: Examination of 2 different aurone treatments in Candida albicans cells. (Three untreated samples, Three SH1009-treated samples, and Three SH9051-treated samples).

middle: M

first: Mary

middle: B

last: Farone

first: Scott

middle: T

last: Handy


title: Piwi–piRNA complexes induce stepwise changes in nuclear architecture at target loci

status: Public on Jul 01 2021

city: Tokyo

first: Yuka

middle: W.

last: Iwasaki

address: 35 Shinanomachi, Shinjuku-ku,

department: Department of Molecular Biology

institute: Keio University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: PIWI-interacting RNAs (piRNAs) are germline-specific small RNAs that form effector complexes with PIWI proteins (Piwi–piRNA complexes), and plays a critical role for preserving genomic integrity by repressing transposable elements (TEs). Drosophila Piwi transcriptionally silences specific targets through heterochromatin formation, and increases H3K9me3 and histone H1. Additionally, Nxf2, a nuclear RNA export factor variant, has been identified as a co-factor. Using ChEP and DamID-seq, we uncover Piwi/Nxf2-dependent target association with nuclear lamins. Hi-C analysis of Piwi or Nxf2 depleted cells reveals decreased intra-TAD and increased inter-TAD interaction in regions harboring Piwi–piRNA target TEs. Using a forced tethering system, we analyze the functional effects of Piwi–piRNA/Nxf2-mediated recruitment of piRNA target regions to the nuclear periphery. Removal of active histone marks is followed by transcriptional silencing, chromatin conformational changes, and H3K9me3 and H1 association. Our data show that the Piwi–piRNA pathway can induce stepwise changes in nuclear architecture and chromatin state at target loci for transcriptional silencing.

overall_design: Lamin-DamID-seq, Hi-C, and ChIP-seq upon knockdown of Piwi-piRNApathway factors using OSCs.

middle: W

first: Haruhiko

last: Siomi


title: RNA-seq of C3H/He mice on the American Lifestyle diet (ALIOS)

city: Newcastle Upon Tyne

first: Helen

last: Reeves

address: Framlington Place

department: Faculty of Medical Sciences

country: United Kingdom

institute: Northern Institute for Cancer Research

summary: We have developed a novel murine model of Diet-induced HCC via feeding the C3H/He mouse strain with the American life style diet (ALIOS) for 48 weeks. RNAseq was performed to the developed tumors as well as the non-tumor tissue of mice livers seeking for understanding the contributing pathways to the development and the progression of HCC in this mice strain. We also investigated whether the tumors developed in mice recaptiulate any particular human HCC subclass.

overall_design: RNA-seq of non-tumor and tumor tissues of mice fed on Amercan lifestyle diet and control diet with/without concurrent admistration of the liver carcinogen DEN

first: Marco

middle: Y

last: Zaki

first: Ahmed

middle: K

last: Mahdi

first: Gillian

last: Patman

first: Anna

last: Whitehead

first: Joao

last: Mauricio

first: Misti

middle: V

last: McCain

first: Despina

last: Televantou

first: Sameh

last: Abou-Beih

first: Robyn

last: Watson

first: Jack

last: Leslie

first: Olivier

last: Govaere

first: John

last: Lunec

first: Derek

last: Mann

first: Sirintra

last: Nakjang

first: Fiona

last: Oakley

first: Ruchi

last: Shukla

first: Quentin

last: Anstee

first: Dina

last: Tiniakos


title: Hepatocyte-specific Genomic and Transcriptional Profiling of NASH and liver fibrosis

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

overall_design: Refer to individual Series


title: MethylC-capture sequencing and RNA sequencing of control (CTL), chronic nonbacterial prostatitis (CNP) and polysaccharide (PPs)-treated SD rats

status: Public on Jun 25 2021

city: guangzhou

first: Ruiqiang

last: Yan

address: 黄埔大道西601号

country: China

institute: Jinan University

type: Methylation profiling by high throughput sequencing


title: Large-scale Chemical Screen Identifies a Geroprotective Role of Gallic Acid in Premature Aging [RNA-seq]

city: Beijing

first: jiang

middle: xiao

last: yu

address: 15 Datun Road Chaoyang District

institute: institute of zoology, CAS

summary: Gallic acid (GA) is a natural phenolic compound with antioxidant, anti-inflammatory, and antineoplastic  properties. Previous studies also revealed that GA supplementation inhibit the decline of rat embryonic and rejuvenate the immune function in D-gal-induced aging accelerated mice. However, the role of GA in regulating senescence of human premature aging stem cells is unknown. We have demonstrated that GA showed beneficial effects in alleviating human mesenchyme stem cell(hMSC) senescence: (1) GA alleviated senescence by promoting stem cell self-renewal ability and down-regulating the expression of aging markers, including P16 and P21, in Werner syndrome(WS) hMSCs; (2) High levels of reactive oxygen species in total cell as well as mitochondria were both rescued by GA treatment; (3) GA also maintained epigenetic features, enhanced cell stemness, and improved mitochondrial homeostasis in WS hMSCs. Our data provide substantial evidence supporting that GA is a promising candidate agent to

overall_design: In Werner syndrome (WS) hMSCs, DMSO-treated cells, GA (gallic acid)-treated cells. Among Hutchinson-Gilford progeria syndrome (HGPS) hMSCs, DMSO-treated cells, GA-treated cells.

first: Guanghui

last: Liu


title: Cell Type-Resolved Genomic Profiling of NASH and liver fibrosis

summary: We generated hepatocyte-specific profiles of the genomic landscapes during NASH progression using the INTACT methodology

overall_design: We fed male HEP-INTACT mice two different NASH-inducing diets, 20 weeks of a FPC diet (Wang et al., 2016) or 7 weeks of a CDAHFD (Matsumoto et al., 2013), and control mice were fed a low fat diet for the same periods. Mice that had been fed NASH-inducing diets were divided into two groups, a mild and advanced NASH group, based on the liver histology. Whereas both groups had high levels of steatosis and inflammation compared to the control group, only the advanced NASH group displayed a significant degree of liver fibrosis. Livers were subsequently subjected to INTACT followed by ATAC-seq analyses.

first: Riccardo

last: Berutti

first: Stephan

last: Herzig


title: Severe COVID-19 is Characterized by an Impaired Type I Interferon Response and Elevated Levels of Arginase Producing Granulocytic Myeloid Derived Suppressor Cells

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

summary: COVID-19 ranges from asymptomatic in 35% of cases to severe in 20% of patients. Differences in the type and degree of inflammation appear to determine the severity of the disease. Recent reports show an increase in circulating monocytic-myeloid-derived suppressor cells (M-MDSC) in severe COVID 19 that deplete arginine but are not associated with respiratory complications. Our data shows that differences in the type, function and transcriptome of granulocytic-MDSC (G-MDSC) may in part explain the severity COVID-19, in particular the association with pulmonary complications. Large infiltrates by Arginase 1+ G-MDSC (Arg+G-MDSC), expressing NOX-1 and NOX-2 (important for production of reactive oxygen species) were found in the lungs of patients who died from COVID-19 complications. Increased circulating Arg+G-MDSC depleted arginine, which impaired T cell receptor and endothelial cell function. Transcriptomic signatures of G-MDSC from patients with different stages of COVID-19, revealed that asymptomatic patients had increased expression of pathways and genes associated with type I interferon (IFN), while patients with severe COVID-19 had increased expression of genes associated with arginase production, and granulocyte degranulation and function. These results suggest that asymptomatic patients develop a protective type I IFN response, while patients with severe COVID-19 have an increased inflammatory response that depletes arginine, impairs T cell and endothelial cell function, and causes extensive pulmonary damage. Therefore, inhibition of arginase-1 and/or replenishment of arginine may be important in preventing/treating severe COVID-19.

overall_design: We did RNA-seq in Covid-19 patients (4 severe, 4 asymptomatic, 4 convalescent) and controls (n=4). RNA was extracted from purified granulocytic-myeloid derived suppressor cells (G-MDSC), qualified by Agilent 2100 and quanitfied by Qubit. Librarires were prepared using the Illumina's TruSeq Stranded mRNA kit and sequenced at 2 x 75bp (50M reads/sample)

first: Matthew

middle: J

last: Dean

first: Juan

last: Ochoa

first: Maria

last: Sanchez-Pino

first: Jone

last: Garai

first: Luis

last: Del Valle

first: Dorota

last: Wyczechowska

first: Lyndsey

last: Buckner Baiamonte

first: Phaethon

last: Philbrook

first: Rinku

last: Majumder

first: Richard

last: Vander Heide

first: Logan

last: Dunkenberger

first: Ramesh

last: Thylur

first: Robert

last: Nossaman

first: W

last: Roberts

first: Andrew

last: Chapple

first: Jiande

last: Wu

first: Chindo

last: Hicks

last: Collins

first: Brian

last: Luke

first: Randall

last: Johnson

first: Hari

last: Koul

first: Chris

middle: A

last: Rees

first: Claudia

last: Morris

first: Julia

last: Garcia-Diaz

first: Augusto

middle: C


title: Epithelial cell plasticity drives endoderm formation during gastrulation

status: Public on Jun 24 2021

city: Garching

first: Maren

last: Büttner

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

summary: We performed 3 single-cell RNAseq experiments to identify the mechanisms of definitive endoderm formation during gastrulation. To enrich for the rare endoderm and endoderm progenitor populations we used the FVF reporter mouse line. 103 homozygous FVF embryos were isloated at two consecutive days: 40 early to mid streak stage embryos at day 1, 39 early to mid streak embryos at day 2 , 24 mid streak to late streak embryos at day 2 . Embryonic compartments from each sample were  FACS sorted according to Foxa2-Venus fluorescence intensity into FVF negative, FVF low and FVF high cell populations. Using the FVF-sorted cell populations we could identify FVF low endoderm progenitors and their continous transition into FVF high anterior defintive endoderm.

overall_design: 3 single-cell RNA-seq experiments were performed using 10X Genomics technology to generate  single cell transcriptomic profiles of gastrulating mouse embryos. Homozygous FVF embryos were sorted to enrich for FVF low and high cell populations.

first: Katharina

last: Scheibner

first: Ingo

last: Burtscher

first: Silvia

last: Schirge

first: Anika

last: Böttcher

first: Sophie

last: Tritschler

first: Michael

last: Sterr

first: Dapeng

last: Yang

first: Martin

last: Irmler

first: Johannes

last: Beckers

first: Filippo

last: Cernilogar

first: Gunnar

last: Schotta

first: Fabian

last: Theis

first: Heiko

last: Lickert


title: RIPK3 Activation Induces TRIM28 Derepression in Cancer Cells and  Enhances the Anti-tumor Microenvironment

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

summary: We identified TRIM28 as a co-repressor that regulates transcriptional activity during necroptosis. RIPK3 activation induces TRIM28 phosphorylation at serine 473, inhibiting its chromatin binding activity, thereby contributing to the transactivation of NF-κB and other transcription factors, such as SOX9. This leads to elevated cytokine expression, which then potentiates immunoregulatory processes, such as DC maturation. The expression of RIPK3 has a significant positive association with the tumor-infiltrating immune cells populations in various tumor type, thereby activating anti-cancer responses.

overall_design: ChIP-seq of HT29 cells as described

first: Jae-Seok

first: Hwa-Ryeon

last: Kim


title: Puf6 primes nuclear export of 60S pre-ribosomes at low temperature

city: Edinburgh

first: Sander

last: Granneman

address: Max Born Crescent, CH Waddington Building

department: Centre for Synthetic and Systems Biology (SynthSys)

institute: University of Edinburgh

summary: Puf6 contributes to biogenesis of the large subunit in yeast. UV-crosslinking (CRAC) was used to determine binding sites of Puf6 on RNA.

overall_design: Duplicate data-sets of cDNA reads of RNAs UV-crosslinked to PUF6-HTP in vivo using the CRAC protocol. Cells were in mid-log phase when irradiated, immediately collected by filtration and frozen

first: Rob

last: van Nues


city: Neuherberg

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

institute: Helmholtz Zentrum München German Research Center for Environmental Health

summary: It is generally accepted that epiblast cells ingress into the primitive streak by epithelial-to-mesenchymal transition (EMT) to give rise to the mesoderm; however, it is less clear how the endoderm acquires an epithelial fate. Here, we used embryonic stem cell and mouse embryo knock‐in reporter systems to combine time-resolved lineage labelling with high-resolution single-cell transcriptomics. This allowed us to resolve the morphogenetic programs that segregate the mesoderm from the endoderm germ layer. Strikingly, while the mesoderm is formed by classical EMT, the endoderm is formed independent of the key EMT transcription factor Snail1 by mechanisms of epithelial cell plasticity. Importantly, forkhead box transcription factor A2 (Foxa2) acts as an epithelial gatekeeper and EMT suppressor to shield the endoderm from undergoing a mesenchymal transition. Altogether, these results not only establish the morphogenetic details of germ layer formation, but also have broader implications for stem cell differentiation and cancer metastasis.

overall_design: We performed Affymetrix microarray analysis on FACS purified TGFP/+; Foxa2tagRFP/+ mESCs, differentiated to definitive endoderm and mesoderm cells at days two and four of differentiation. FACS was based on GFP, tagRFP and CD24 levels.

first: Katharina

last: Scheibner

first: Ingo

first: Maren

last: Büttner


title: PRMT1-dependent regulation of RNA metabolism and DNA damage response is a critical dependency in pancreatic ductal adenocarcinoma

city: Davis

first: Frederic

last: Chedin

address: 1 Shields Avenue

department: MCB

institute: UC Davis

summary: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer, which represents a critical area of unmet need for novel therapeutic options.  Here we deployed an RNAi-based in vivo functional genomics platform to identify epigenetic vulnerabilities across a panel of patient-derived PDAC models.  Through this effort, we identified protein arginine methyltransferase 1 (PRMT1) as a critical dependency required for PDAC maintenance.  Genetic and pharmacological studies validated the role of PRMT1 in maintaining PDAC growth and informed the mechanism-of-action through proteomic and transcriptomic analyses.  Mechanistically, we showed that inhibition of asymmetric arginine methylation globally impaired RNA metabolism, including RNA splicing, alternative polyadenylation, and transcription termination, causing a profound down-regulation of multiple pathways involved in the DNA damage response, thereby promoting genomic instability and inhibiting tumor growth. Taken together, these data support PRMT1 as a compelling target in PDAC and inform a mechanism-based translational strategy for future therapeutic development.

overall_design: Identification of PRMT1 as a unique vulnerability in patient-derived PDAC model in vivo using pharmacological and genetic techniques, and characterization of R-loop and transcription landscape in PRMT1 Inhibited PANC1 and PATC53 cells using polyA RNA-seq and sDRIP seq.

first: Virginia

last: Giuliani

first: Meredith

last: Miller

first: Chiu-Yi

last: Liu

first: Stella

last: Hartono

first: Caleb

last: Class

first: Christopher

last: Bristow

first: Erika

last: Suzuki

first: Lionel

last: Sanz

first: Guang

last: Gao

first: Jason

middle: P

last: Gay

first: Ningping

last: Feng

first: Jonathon

last: Rose

first: Hideo

last: Tomihara

first: Joseph

last: Daniele

middle: D

last: Peoples

first: Jennifer

last: Bardenhagen

first: Mary

last: Geck Do

first: Edward

middle: Q

last: Chang

first: Bhavatarini

last: Vangamudi

last: Vellano

first: Haoqiang

last: Ying

first: Angela

last: Deem

first: Kim-Anh

last: Do

first: Giannicola

last: Genovese

last: Marszalek

first: Jeffrey

last: Kovacs

last: Fleming

first: Ernesto

last: Guccione

first: Andrea

last: Viale

first: Anirban

last: Maitra

first: Maria

last: Di Francesco

first: Timothy

last: Yap

first: Philip

last: Jones

first: Giulio

last: Draetta

first: Alessandro

last: Carugo


title: Transcriptome sequencing in serum exosomes from proliferative diabetic retinopathy (PDR)

city: Nanjing

first: Ping

last: Xie

state: jiangsu

address: 300 Guangzhou Road

department: department of ophthalmology

institute: The First Affiliated Hospital of Nanjing Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: To detect serum exosomal ncRNA profiles of proliferative diabetic retinopathy (PDR) by High-throughput sequencing
Methods: serum exosomal non-coding RNA (ncRNA) profiles profiles of PDR and MH were generated by deep sequencing, only in once, using IlluminaHiSeq 3000. After analyzing the base composition and quality of the data, according to the analysis results of the original data, the data were filtered  to remove the joint sequence and the contaminated part, and to remove  low-quality base sequences.If it is paired-ended sequencing data, the filtered data should be further screened to retain the paired sequences and obtain clean data.
Conclusions: Our study represents the first detailed analysis of serum exosomal transcriptomes from PDR patients by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.

overall_design: Serum exosomal non-coding RNA (ncRNA) profiles from two samples consisted ten proliferative diabetic retinopathy patients and ten macular hole patients as control group

first: Zizhong

last: Hu

first: Huiming

last: Qian

first: Xinsheng

last: Li


title: MethylC-capture sequencing and RNA sequencing of control (CTL), chronic nonbacterial prostatitis (CNP) and polysaccharide (PPs)-treated SD rats [RNA-Seq]

first: Ruiqiang

last: Yan

summary: SD rats were intramuscular injected with dexamethasone to induce osteCPorosis, and treated with APS. Then, colonic epithelia of control, osteCPorotic and APS-treated osteCPorotic rats were collected for MethylC-capture sequencing .

overall_design: RNA-seq examination of colonic epithelia of  three groups of rats

first: Junsheng

last: Liu

first: Xichun

last: Peng


title: Effect of enzymatically-hydrolysed eggshell membrane (eESM) in Human keratinocyte

status: Public on Jun 22 2021

city: Nagoya

first: Kyohei

last: Furukawa

address: Furo-cho, Chikusa-ku

institute: Nagoya University

summary:
Skin aging is one of the hallmarks of the aging process that causes physiological and morpho-logical changes. Recently, several nutritional studies were conducted to delay or suppress the aging process. This study investigated whether nutritional supplementation of the eggshell membrane (ESM) has a beneficial effect on maintaining skin health and improving the skin ag-ing process  using neonatal normal human epidermal keratinocytes (NHEK-Neo).
1 mg/mL of enzymatically hydrolyzed ESM (eESM) upregulated the expression of keratinocyte differentiation markers, including keratin 1, filaggrin and involucrin, and changed the keratinocyte morphology.

overall_design: Neonatal Normal Human Epidermal Keratinocytes (NHEK-Neo) were incubated with control medium or 1 mg/ml of eESM-supplemented medium for 4 days. N value of each group was three.

first: Hisanori

last: Kato


title: Enzymatically-hydrolysed eggshell membrane (eESM) in Human keratinocyte - Eggshell membrane powder (pESM)-supplemented IL-10 KO mice

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: High-resolution, genome-wide mapping of positive supercoiling in chromosomes

city: Seattle

first: Monica

middle: S

last: Guo

state: WA

address: 750 Republican St

department: Microbiology

institute: University of Washington

sample_organism: Escherichia coli str. K-12 substr. MG1655


title: Secretory microRNA profiles of third- and fourth-stage Dirofilaria immitis larvae with different macrocyclic lactone-susceptibility: in search for biomarkers for early-detection of infection

status: Public on Jun 21 2021

city: Sainte-Anne-de-Bellevue

first: Lucienne

last: Tritten

state: QC

address: 21111 Lakeshore Road

department: Institute of Parasitology

country: Canada

institute: McGill University

summary: We cultured D. immitis L3 and L4 of two laboratorial strains with different susceptibility status to macrocyclic lactone drugs in vitro. Excretory/secretory microRNAs were sequenced and analyzed.

overall_design: D. immitis L3 and L4 of two different strains were allowed to excrete/secrete miRNAs in vitro, which were profiled by miRNA sequencing and compared.

first: Erica

last: Burkman

first: Tobias

last: Clark

first: Guilherme

middle: G

last: Verocai


title: Expression data from eggshell membrane powder (pESM)-supplemented IL-10 KO mice

summary:
Skin aging is one of the hallmarks of the aging process that causes physiological and morpho-logical changes. Recently, several nutritional studies were conducted to delay or suppress the aging process. This study investigated whether nutritional supplementation of the eggshell membrane (ESM) has a beneficial effect on maintaining skin health and improving the skin aging process  in  interleukin-10 knockout (IL-10 KO) mice.
Oral supplementation of 8% powdered-ESM (pESM) upregulated the expression of growth factors, including transforming growth factor β1, platelet-derived growth factor-β and connective tissue growth factor, and suppressed skin thinning.

overall_design: Four-week-old WT (C57BL/6J) and KO (Interleukin-10 knockout)  mice were fed an AIN-93-based diet or an 8% pESM-supplemented diet for 28 weeks. After the experimental period, the back skin was collected under deep anesthesia with isoflurane, removed the dermal white adipose tissue from collected skin sample. The n value is 5, 7 and 6 for WT, KO and KO + pESM (KOE groups), respectively.


title: RBFOX2 alter splicing outcome in distinct binding modes with multiple protein partners

status: Public on Jun 23 2021

city: Sherbrooke

first: Michelle

last: Scott

state: Quebec

address: 3201, rue Jean-Mignault

institute: University of Sherbrooke

summary: RBFOX2 controls the splicing of a large number of transcripts implicated in cell differentiation and development. Parsing RNA-binding protein datasets, we uncover that RBFOX2 can interact with hnRNPC, hnRNPM and SRSF1 to regulate splicing of a broad range of splicing events using different sequence motifs and binding modes. Using immunoprecipitation, specific RBP knockdown, RNA-seq and splice-sensitive PCR, we show that RBFOX2 can target splice sites using three binding configurations: single, multiple or secondary modes. In the single binding mode RBFOX2 is recruited to its target splice sites through a single canonical binding motif, while in the multiple binding mode RBFOX2 binding sites include the adjacent binding of at least one other RNA binding protein partner. Finally, in the secondary binding mode RBFOX2 likely does not bind the RNA directly but is recruited to splice sites lacking its canonical binding motif through the binding of one of its protein partners. These dynamic modes bind distinct sets of transcripts at different positions and distances relative to alternative splice sites explaining the heterogeneity of RBFOX2 targets and splicing outcomes.

overall_design: Each of the four RBPs (RBFOX2, hnRNPC, hnRNPM and SRSF1) were depleted using 2 different siRNA in 2 biological replicates. Lipofectamine (lipo) samples serve as mock control.

first: Delong

last: Zhou

first: Sonia

last: Couture

first: Sherif

last: Abou Elela


title: ChIP-seq and RNA-seq analysis of histone Kcr in the embryonic forebrain and neural stem/progenitor cells.

city: Zibo

first: Dai

middle: Shang

last: Kun

state: Shandong

address: 266 Xincun West Road

department: School of Life Sciences and Medicine

institute: Shandong University of Technology

summary: To gain a deeper insight into how histone lysine crotonylation regulates embryonic neural stem/progenitor cells (NSPCs) proliferation and differentiation, ChIP-seq and RNA-seq were performed to analyze the genome-wide changes of histone Kcr and transcriptiome changes stimulated with crotonate and MS-275 in E13.5 NSPCs.

overall_design: Total RNA was extracted from E13.5 NSPCs before and after crotonate and MS-275 stimulation and generated by deep sequencing, in four biological replicates, using Illumina novaseq 6000. ChIP was excuted using pan-Kcr and Pan-Kac antibody with E13.5 NSPCs before and after crotonate and MS-275 stimulation.

first: Shang-Kun

last: Dai

first: Chang-Mei


title: Defining AP4-regulated gene expression programs in pro/pre-B cells overexpressing c-MYC

status: Public on Jun 19 2021

city: Saint Louis

first: Takeshi

last: Egawa

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: A hallmark feature of adaptive immune cells is their capacity for rapid cell proliferation required for producing and expanding cells with a diverse repertoire of antigen receptor and amplification of antigen-specific receptors. While proliferation is beneficial for host protection from infection and cancers, it inevitably elevates the risk of oncogenic transformation. Developing lymphocytes, as well as B cells in the germinal center (GC), are considered tumor-prone due to additional genomic insults from physiological antigen receptor gene rearrangement and editing. However, oncogenic transformation of lymphocytes is relatively rare, perhaps owing to an intrinsic, tumor-suppressive program. Here, we show that c-MYC not only facilitates rapid cell proliferation but, unexpectedly, also engages a counteracting tumor suppressive program through its downstream transcription factor, AP4. Haploinsufficiency for AP4 dramatically accelerates MYC-driven tumorigenesis in a B cell-intrinsic manner. At a mechanistic level, AP4 suppresses Erg, which is required for B cell development but also oncogenic, in MYC+ developing B cells, and thus AP4 restricts simultaneous expression of multiple oncogenic factors during B cell development. Thus, c-MYC has dual action that permit proliferative expansion of B cell precursors, while concurrently safeguarding against their transformation via engagement of an AP4-dependent, tumor-suppressive program.

overall_design: B220+IgM– pro/pre B cells from EuMyc or EuMyc Tfap4 heterozygous mice were isolated at 3-4 weeks of age, prior to tumor development, or from developed tumors and gene expression, AP4 occupancy, and H3K27ac deposition was analyzed with n=2-5 biological replicates.


title: RHOX10 Drives Mouse Spermatogonial Stem Cell Establishment Through A Transcription Factor Signaling Cascade

status: Public on Jun 18 2021

city: La Jolla

first: Kun

last: Tan

address: 2880 Torrey Pines Scenic Dr. Room 4812

department: Department of Obstetrics, Gynecology, and Reproductive Sciences

institute: UCSD

summary: Spermatogonial stem cells (SSCs) are essential for male fertility. Here, we report that mouse SSC generation is driven by a transcription factor (TF) cascade controlled by the homeobox protein, RHOX10, which acts by stimulating the differentiation of SSC precursors called pro-spermatogonia (ProSG). We identify genes regulated by RHOX10 in ProSG in vivo, and define direct RHOX10-target genes using several approaches, including a rapid temporal induction assay we design: iSLAMseq. Together, these approaches identify temporal waves of direct targets, as well as secondary-target genes. Many of the RHOX10-regulated genes encode proteins with known roles in SSCs. Using an in vitro ProSG differentiation assay that we develop, we find that RHOX10 promotes mouse ProSG differentiation through a conserved transcriptional cascade involving the key germ-cell TFs DMRT1 and ZBTB16. Our study gives important insights into germ cell development and provides a blueprint for how to define TF cascades.

overall_design:
RNAseq: Mice were crossed with OCT4-eGFP mice. eGFP+ cells were sorted by fluorescence-activated cell sorting (FACS). For each sample analyzed, testes from 3 individuals were pooled. Four replicate samples were analyzed per genotype.
CUT&Tag: Mouse germline stem (GS) cells were dissociated from neonatal testes. Endogenous RHOX10 was knocked-down using an shRNA lentivirus and purified on the basis of GFP fluorescence by FACS. A HA-tagged Rhox10 lentivirus (unsensitive to this shRNA; expresses mCHERRY reporter) was used to induce a control level of exogenous Rhox10 expression. 1 million GS cells were used per sample and three biological replicates were performed. The negative IgG controls were performed using Rhox10-kd;HA-tagged Rhox10 GS cells.  Samples from Rhox10-kd; HA-tagged empty vector GS cells served as another control (Ctrl).
iSLAMseq: Endogenous Rhox10 in mouse GS was knocked-down using an shRNA lentivirus and purified on the basis of GFP fluorescence by FACS. A lentivirus expression vector carrying the Rhox10-ERT2-mCherry fusion gene was used to make a conditional inducible Rhox10 expression in response to 4-Hydroxytamoxifen. 2 millions GS cells were prepared for each sample, six time points with two biological replicates were performed. Samples from Rhox10-kd; ERT2-mCherry empty vector served as the control.

first: Miles

middle: F

last: Wilkinson


title: The ChIP_seq of pituitary gland from Bama Xiang and Large White pigs

city: Nanchang

first: Zhimin

address: 888 Lushan Middle Avenue

institute: 江西农业大学

summary: we performed chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to profile histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac) in pituitary gland of adult Bama Xiang and Large White pigs with divergent evolutionary histories and large phenotypic differences.

overall_design: ChIP-seq analysis in Pituitary Gland of Bama Xiang and Large White Pigs


title: RNAseq from cuticles of tumor free (w1118) and tumor bearing Drosophila larvae (MARCM RasV12, scrib1) tumour-bearing Drosophila larvae

status: Public on Jun 17 2021

city: Glasgow

first: Julia

last: Cordero

state: Please select your county

address: Garscube Estate. Switchback Road

institute: University of Glasgow

summary: To investigate which factors might be driving the cachectic muscle wasting observed in our larval models bearing RasV12, scrib1 tumors, we performed RNA sequencing (RNAseq) on the cuticles of wild type and RasV12, scrib1 tumour-bearing larvae. Pathway and gene ontology analysis revealed significant deregulation of stress and starvation response genes, metabolic genes, and inflammation and immune regulatory genes within cachectic muscle of tumour bearing larvae.

overall_design: Cuticles were dissected in freshly autoclaved PBS and all internal tissues were removed to keep only the body wall including the skeletal muscles (40 cuticles/sample). Cuticles were frozen in a collection tube placed on dry ice. Total RNA was extracted using QIAGEN RNAeasy kit, following the manufacturer’s instructions, including the on-column DNase digestion step. For RNA-seq an RNA integrity score was determined to check RNA quality C11(Agilent technologies 2200 Tapestation, RNA Screen Tape).

first: Joseph-Alexander

last: Hodgson

first: Jean-Philippe

last: Parvy


city: Baltimore

first: Alan

middle: E.

last: Berger

state: MD

address: 5501 Hopkins Bayview Circle Room 3B.74C

institute: Johns Hopkins University

summary:
Viruses are the second leading cause of cancer worldwide, and human papillomavirus (HPV)-associated head and neck cancers are increasing in incidence in the United States. HPV preferentially infects the crypts of the tonsils rather than the surface epithelium. The present study sought to characterize the unique microenvironment within the crypts to better understand the host tropism of HPV to a lymphoid rich organ. Laser-capture microdissection of distinct anatomic areas (crypts, surface epithelium, and germinal centers) of the tonsil coupled with transcriptional analysis and multi-parameter immunofluorescence staining was performed and demonstrated that the tonsillar crypts are enriched with myeloid populations which co-express multiple canonical and non-canonical immune checkpoints, including PD-L1, CTLA-4, HAVCR2 (TIM-3), ADORA2A, IDO1, BTLA, LGALS3, CDH1, CEACAM1, PVR, and C10orf54 (VISTA).  The resident monocytes may foster a permissive microenvironment that facilitates HPV infection and persistence. Furthermore, the myeloid populations within HPV-associated tonsil cancers co-express the same immune checkpoints, providing insight into potential novel immunotherapeutic targets for HPV-associated head and neck cancers.
The associated paper "Myeloid cells are enriched in tonsillar crypts providing insight into the host tropism of HPV", Austin K. Mattox, Jessica Roelands, Talia Saal, Yang Cheng, Darawan Rinchai, Wouter Hendrickx, Geoffrey D. Young, Thomas J. Diefenbach, Alan E. Berger, William H. Westra, Justin A. Bishop, William C. Faquin, Francesco M. Marincola, Mikael J. Pittet, Davide Bedognetti, and Sara I. Pai; The American Journal of Pathology, Online ahead of print DOI:https://doi.org/10.1016/j.ajpath.2021.06.012

overall_design: Tissue was obtained from the tonsils of 4 patients who underwent tonsillectomy for benign disease. Tissue from the tonsillar crypts, lymphoid stroma, and surface epithelium was obtained from each of these samples by laser capture microdissection.  Gene expression levels were compared between these tissue compartments

first: Austin

last: Mattox

first: Jessica

last: Roelands

first: Talia

last: Saal

first: Yang

last: Chen

first: Darawan

last: Rinchai

first: Wouter

last: Hendrickx

first: Geoffrey

last: Young

first: Thomas

last: Diefenbach

middle: E

first: William

middle: H

last: Westra

first: Justin

last: Bishop

last: Faquin

first: Francesco

middle: M

last: Marincola

first: Mikael

last: Pittet

first: Davide

last: Bedognetti

first: Sara

middle: I

last: Pai


title: Microarray analysis of mouse retinal organoids

city: Kobe

first: Takesi

last: Matsuyama Hoyos

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuou-ku

department: BDR

institute: RIKEN

summary: ES/iPS-retinal sheet transplantation, which supplies photoreceptors as well as other retinal cells, has been shown able to restore visual function in mice with end-stage retinal degeneration. Here, we introduce a novel type of genetically engineered mouse ES/iPS-retinal sheet with reduced numbers of secondary retinal neurons but intact photoreceptor cell layer structure (Bhlhb4 knockout and Islet1 knockout). We show that this KO grafts can differentiate into retinal organoids with similar potency as wildtype retinal organoids. The data set contains data from 3 cell  lines: wildtype (WT, specified as ‘NCT’), B4KO (Bhlhb4 knock-out), and Isl1KO(Islet-1 knockout) across 3 differential days (DDs, DD10, DD16, and DD23) along the early differentiation of retinal tissue.

overall_design:
We compared the expression pattern of retinal organoids that were genetically engineered to reduce the number of bipolar cell numbers. The data set contains data from 3 cell  lines: wildtype (WT, specified as ‘NCT’), B4KO (Bhlhb4 knock-out), and Isl1KO(Islet-1 knockout) across 3 differentian days (DDs, DD10, DD16, and DD23)
RNA was prepared using TRIZOL reagent (thermo fisher), following manufacturers instructions. For each sample, 5 retinal organoids were aggregated to ensure enough RNA was obtained. Extracted RNA was purified using QIAGEN RNeasy Micro Kit and quantified using a NanoDrop-1000 spectrophotometer and  the quality of purified RNA was monitored using Agilent 2100 Bioanalyzer.


title: An integrated functional and clinical genomics approach reveal genes driving aggressive metastatic prostate cancer [ATAC-Seq]

city: San Francisco

first: Raunak

last: Shrestha

department: Radiation Oncology

institute: University of California, San Francisco

summary: Genomic sequencing of many thousands of tumors has revealed many genes associated with specific types of cancer. Similarly, large scale CRISPR functional genomics efforts have mapped genes required for proliferation or survival in hundreds of cancer cell lines. Despite this, for specific disease subtypes, such as metastatic prostate cancer, it is likely that there exist many undiscovered tumor specific genetic dependencies, such as prostate cancer specific drivers, that represent drug targets. To identify such genetic dependencies, we performed genome-scale CRISPRi screens in metastatic prostate cancer models. We then created a pipeline in which we integrated publicly available pan-cancer functional genomics data with our metastatic prostate cancer functional and clinical genomics data to identify genes that can drive aggressive prostate cancer phenotypes. Our integrative analysis of these data revealed two known prostate cancer specific driver genes, AR and HOXB13, as the top two hits and also nominated a number of unexpected genes. In this study we highlight the strength of an integrated clinical and functional genomics pipeline and focus on two hit genes, KIF4A and WDR62. We demonstrate that both KIF4A and WDR62 drive aggressive prostate cancer phenotypes in vitro and in vivo in multiple models, irrespective of AR-status, and are also associated with poor patient outcome.

overall_design: ATAC-seq was performed in KIF4A knockdown in LNCaP and C42B prostate cancer cells

first: Rajdeep

last: Das

first: Felix

middle: Y

last: Feng

first: Luke

last: Gilbert


title: Butyrophilin-like 2 (Btnl2) regulates site-specific adaptations of tissue-resident gd intraepithelial lymphocytes

status: Public on Jun 16 2021

city: Tarrytown

first: Wei Keat

last: Lim

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

summary:
Background: Tissue-resident gd intraepithelial lymphocytes (IELs) orchestrate innate and adaptive immune responses to maintain intestinal epithelial barrier integrity. Epithelia-specific butyrophilin-like (Btnl) molecules induce perinatal development of distinct Vg TCR+ IELs, however, the mechanisms that control gd IEL maintenance within discrete intestinal segments are unclear. Btnl2, a member of Btnl family, has been shown to induce Treg differentiation and suppress T cell activation and proliferation in vitro. Btnl2 is highly enriched in villous IECs across different intestinal compartments and its expression is reported to be altered by inflammatory cues such as epithelial injury and tumor burden. We sought to understand the role of Btnl2 in regulating intestinal immune responses during homeostasis and inflammation and, particularly, in the induction and maintenance of intestinal gd IELs.
Methods: We surveyed the gut immune system of in-house generated Btnl2-KO and WT mice within discrete intestinal segments (duodenum, jejunum, ileum, colon) during homeostasis and DSS-induced epithelial injury using flow cytometry, primary cell assays, immunoassays, and gene expression profiling. In addition, we performed high throughput transcriptomic (bulk RNAseq and scRNAseq) and TCR repertoire (scTCRseq) characterization of segment-specific Btnl2-KO and WT gd IELs at steady-state.
Results: We characterized newly generated Btnl2 knockout mice and identify a role for Btnl2 in regulating the frequencies and phenotype of gd IELs preferentially in the ileum at steady state. We found that gd IELs derived from the ileum, but not duodenum, of Btnl2-KO mice possess a dysregulated antibacterial response module. By integrating RNA and single-cell TCR expression data we identified distinct transcriptional signatures and greater TCR repertoire diversity in ileal Btnl2-KO gd IELs. Upon DSS challenge, Btnl2-KO mice displayed enhanced colonic, but not ileal, intestinal inflammation and delayed mucosal repair.
Conclusions: Collectively, our findings suggest that context-dependent Btnl2 expression fine-tunes intestinal immune responses to protect against epithelial injury. Overall, Btnl-mediated targeting of γδ IEL development and maintenance may help dissect their immunological functions in intestinal diseases with segment-specific manifestations.

first: Casandra

last: Panea

first: Ruoyu

last: Zhang

first: Jeffrey

last: VanValkenburgh

first: Susan

last: Chyou

first: Min

last: Ni

first: Christina

last: Adler

first: Qi

last: Zhao

first: Yi

last: Wei

first: Sarah

last: Voor

first: Jennifer

last: Espert

first: Francisca

last: Ochoa

last: Schmahl

last: Poueymirou

first: Nicole

last: Oristian

first: Wei

middle: K

first: Gurinder

last: Atwal

first: Andrew

last: Murphy

first: Matthew

last: Sleeman

first: Zaruhi

last: Hovhannisyan

first: Sokol

last: Haxhinasto


title: An integrated functional and clinical genomics approach reveal genes driving aggressive metastatic prostate cancer

first: Raunak

last: Shrestha

overall_design: Refer to individual Series


title: FLAG-tagged hnRNPM iCLIP in AGS cells

city: hefei

first: Xiaolin

last: Wang

address: anhui,hefei,huangshan road 443

institute: USTC

summary: We performed hnRNPM iCLIP to identify the potential targets.

overall_design: Briefly, 5,000,000 AGS cells expressing FLAG-hnRNPM were ultraviolet crosslinked to a total of 0.4 J/cm2 in a UV cross-linker and harvested in ice-cold lysis buffer (10 mM HEPES (pH 7.4), 200 mM NaCl, 30 mM EDTA, 0.5% Triton-X 100, 1.5 mM DTT and 1× Protease-inhibitor cocktail (Roche, 04693116001)). Then, cells were sonicated for 5 min with a Sonics Vibra-Cell, and the cell supernatant was collected after centrifugation at 12,000 g for 15 min at 4 °C. The hnRNPM-binding complex was isolated by anti-FLAG (Sigma, F1804) coupled with Protein G Dynabeads (Life Technology, 10004D) and partially digested with 0.1U/μl RNase I (Thermo Scientific, EN0601) for 3 min at 37 °C. After washing once with lysis buffer, twice with high salt lysis buffer (10 mM HEPES (pH 7.4), 500 mM NaCl, 30 mM EDTA, 0.5% Triton-X 100, 1.5 mM DTT, 50 U/ml RNasin Inhibitor (Promega, N2111SV) and 1× Protease-inhibitor cocktail), RNAs were dephosphorylated at the 3’ ends by T4 polynucleotide kinase (NEB, M0201L) for 20 min at 37 °C and then ligated at their 3’ ends to a preadenylated DNA linker (5’-rApp-AGATCGGAAGAGCACACGTCTGAAC/AzideT/CCAGTCAC-3’) with T4 RNA ligase I (NEB, M0204) for 60 min at 25 °C. The IR800CW dye conjugated to the NHS-Azide modification (/AzideT/) could be visualized using near infrared imager (Kaczynski et al., 2019). SDS-PAGE separation, visualization, protein-RNA complexes isolation, proteinase K treatment, and overnight RNA precipitation were performed as previously described (Kaczynski et al., 2019). For iCLIP cDNA library preparation, the isolated RNAs were reverse transcribed with barcoded primers. The cDNA library was purified by PAGE, circularized by CircLigase II (Lucigen, CL9021K), PCR-amplified by NEBNext Ultra II Q5 Master Mix (NEB, M0544S) for ~25 cycles and then subjected to high-throughput sequencing using an Illumina HiSeq2000 platform with a 50-nt run length.


title: Intron looping is mediated during transcription by U1 snRNP and RNA polymerase II [RNA-Seq]

city: Jerusalem

first: Matan

last: Sorek

address: Edmond J. Safra Campus

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

summary: In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF. The mechanism that facilitates this intron looping is poorly understood. Using a CRISPR interference-based approach to halt RNA polymerase II transcription in the middle of introns, we discovered that the 5 splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. Correlation with splicing outcomes demonstrate that these associations are functional. The interactions between 5 splice sites, U1 snRNP, and elongating RNA polymerase II occurs genome-wide. Our findings reveal that during intron synthesis the upstream 5 splice site remains attached to the transcriptional machinery and is thus brought into proximity of the 3 splice site to enable rapid splicing.

overall_design: RNA-Seq HEK293 cells

first: Yodfat

last: Leader

first: Galit

last: Lev Maor

first: Luna

last: Tammer

first: Ifat

last: Keydat

first: Dror

last: Hollander

first: Eran

last: Meshorer

first: Gil

last: Ast


title: Cell-autonomous Inflammation of BRCA1-deficient Ovarian Cancers Drives Intrinsic Immunoreactivity and Immune Resistance through STING and VEGF

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre hospitalier universitaire vaudois

summary: BRCA1 loss leads to tumor cell transcriptional reprogramming, resulting in a DNA damage-driven, mandatory cell-autonomous type I IFN inflammatory activation mediated by STING and TREX1/2. PARP inhibition augmented this immunoreactivity, creating contextual lethality to dual immune checkpoint blockade (ICB) in vivo. BRCA1-deficient tumor can escape T-cell inflammation through targeted deletion or methylation of the DNA sensing/IFN pathway genes, such as STING, IFNB1 or the chemokine CCL5. Alternatively, BRCA-mutated carcinomas retaining immunoreactivity upregulate their VEGF-A expression driven by STING, which mediates immune resistance and tumor progression. STING elimination attenuated tumor growth and abrogated therapeutic resistance to dual ICB. VEGF-A blockade synergized with immune checkpoint blockade and/or PARP inhibition to control outgrowth of Brca1-/- ovarian tumors, offering opportunities for rational combination therapy of cancers with homologous recombination repair deficiency (HRD).

overall_design: RNAseq analysis of ID8 Trp53-/-Brca1-/- tumors treated with Olaparib and/or/or dual PD-L1/CTLA-4 blockade and/or anti-VEGFA

first: Denarda

last: Dangaj

first: Marine

last: Bruand

first: George

last: Coukos


title: Intron looping is mediated during transcription by U1 snRNP and RNA polymerase II [RIP-seq]

overall_design:
RNA-ChIP-Seq of Pol2-ser2 and U1 and double RNA-ChIP-Seq of Pol2-ser2-U1 with and without AMT treatment

Please note that the processed data for the *_AMT samples is generated from a merged version of both replicates and is linked to the corresponding *rep2 sample records.


title: Intron looping is mediated by U1 snRNP and RNA polymerase II co-transcriptionally


title: Intron looping is mediated by U1 snRNP and RNA polymerase II co-transcriptionally [ChIP-seq]

summary: In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF. The mechanism  that facilitates this intron looping is poorly understood. Using a CRISPR interference-based  approach to halt RNA polymerase II transcription in the middle of introns, we discovered that the 5  splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. Correlation with splicing outcomes demonstrate that these associations are functional. The interactions between 5 splice sites, U1 snRNP, and elongating RNA  polymerase II occurs genome-wide. Our findings reveal that during intron  synthesis the upstream 5  splice site remains attached to the  transcriptional machinery and is thus brought into proximity of the 3  splice site to enable rapid splicing.

overall_design: ChIP-Seq of Pol2-ser2, U1, U2AF65, and double ChIP-Seq of Pol2-ser2-U1, Pol2-ser2-U2AF65, and Pol2-ser2-PTPBP1 in HEK293 cells


title: PARP Inhibition Exacerbates Tumor-autonomous Immunogenicity Driven by BRCA1 Deficiency through DNA Sensing and Interferon Response in Ovarian Cancer

summary: BRCA1 is an essential gene of the homologous recombination repair (HR) pathway. Ovarian cancers with BRCA1 mutations represent about 20% of HGSOC and are characterized by loss-of-function TP53 mutations, copy number alterations, chromosomal instability, high neoantigen loads and increased infiltration of intraepithelial CD8 tumor-infiltrating lymphocytes (TILs). We propose that DNA damage induced by BRCA1 loss could be a tumor-autonomous inflammatory mechanism. Our hypothesis was corroborated by studies in human and mouse isogenic ovarian cancer cell lines which revealed that BRCA1 deficiency leads to increased cytoplasmic gamma H2AX+ double stranded (ds) DNA species, overexpression of proteins of the nucleic acid sensor pathway (IFI16, STING, MX1),  phosphorylation of TBK1, IRF3 and STAT1 and secretion of pro-inflammatory cytokines (IFN-b, IFN-a) and T cell recruiting chemokines (CCL5, CXCL9, CXCL10). PARP inhibition exacerbated type I IFN responses in BRCA1 deficient ovarian cancer cell lines and simultaneously increased surface expression of PDL1. Increased DNA damage, as measured by γH2AX tumor staining, was also detected in situ in human ovarian cancers with BRCA1 mutations.  Importantly, we detected tumor expression of pSTAT1 confirming a type I IFN activation in tumors with DNA damage. Both DNA damage and pSTAT1 activation correlated with higher TIL infiltration and better overall survival.   Our results translated in mouse models of ovarian cancer where Trp53-/-Brca1-/- but not Trp53-/-Brca1WT tumors presented with biomarkers of DNA damage, type I IFN pathway activation and responded to a therapeutic combination of PARP inhibitor Olaparib with dual checkpoint blockade antibodies. Our results provide a mechanistic link between loss of BRCA1 and induction of tumor-driven inflammatory and immunogenic responses in ovarian cancer that was mediated by tumor-cell autonomous type I IFN signaling. which translated to increased immune surveillance by CD8 T cells.

overall_design: The human cell line UWB1.289 which harbors a deleterious mutation in BRCA1 was profiled in triplicates for transcriptomics as well as its isogenic counterpart line with forced expression of wild-type BRCA1 in triplicate.


title: Immunogenicity of BRCA1-deficient Ovarian Cancers is Driven through DNA Sensing and is  Augmented by PARP Inhibition

state: VD

address: Rue du Bugnon 46

department: Department of Oncology

institute: Ludwig Institute for Cancer Research, and University of Lausanne

summary: This SuperSeries is composed of the SubSeries listed below.


title: Immunogenicity of BRCA1-deficient Ovarian Cancers is Driven through DNA Sensing and is  Augmented by PARP Inhibition (ChIP-Seq)

summary: We investigated BRCA1-deficient ovarian cancer to understand why homologous recombination deficiency (HRD) is associated with tumor T-cell inflammation. In humans and mice, BRCA1 deficiency led to increased cytoplasmic translocation of nuclear DNA, increased DNA sensing, induction of proinflammatory cytokines and T-cell recruiting chemokines, and increased tumor CD8+ T-cell infiltration. This cascade was mediated by STING and phosphorylation of TBK1, IRF3 and STAT1. BRCA1 loss activated a transcriptional reprogramming of tumor cells, leading to overexpression of the DNA sensing pathway and hyper-responsiveness to cytoplasmic DNA. Genetic alterations of the DNA sensing and interferon pathways modulated the impact of HRD on T-cell inflammation. PARP inhibitor olaparib exacerbated cytoplasmic DNA and the cell-autonomous inflammatory activation of BRCA1-deficient cancers, and rendered them susceptible to PD-1/CTLA-4 blockade. We conclude that HRD and DNA sensing drives the immunogenicity of ovarian carcinomas and predisposes them to immune vulnerability under immune checkpoint blockade.

overall_design: The human ovarian cancer cell line UWB1.289,which harbors a deleterious mutation in BRCA1 exon11 and LOH, was profiled for transcriptional activation by H3K27Ac CHIP-Seq . Same experimental procedure was followed for UWB1.289 BRCA1 wt reconstituted isogenic pair.

first: Sora

last: Chee

first: Brian

middle: J

last: Stevenson

first: Julien

last: Dorier

first: Bing

last: Ren

first: Christian

last: Iseli


title: CUT&Tag analysis of H3K4me3 and H3K27me3 in the neural stem/progenitor cells under crotonate treatment.

status: Public on Jun 15 2021

first: Dai

last: Kun

summary: To gain a deeper insight into how crotonate regulates embryonic neural stem/progenitor cells (NSPCs) proliferation and differentiation, CUT&Tag was performed to analyze the genome-wide changes of H3K4me3 and H3K27me3 stimulated with crotonate in E13.5 NSPCs.

overall_design: CUT&Tag was performed before and after crotonate treatment, and sequenced on Illumina NovaSeq 6000 platform.

first: Shang-Kun

last: Dai


title: Expression data of HNSCC cell lines grown without and with patient-matched CAFs in 3D

city: Linköping

first: Emilia

last: Wiechec

address: Sandbäcksgatan 7

department: Biomedical and Clinical Sciences

institute: Linköping University

summary:
Cancer associated fibroblasts (CAFs) are the major cellular component of the tumor microenvironment and they have been shown to stimulate tumor growth, epithelial-to-mesenchymal transition (EMT), invasion and radio-resistance.
We used microarrays to investigate the influence of CAFs on the gene expression profile of HNSCC cells in 3D co-cultures

overall_design: HNSCC cells (LK0902, LK0917, LK1108) grown as CAF co-culture in 3D were selected  for RNA extraction and hybridization on Affymetrix microarrays.

first: Karin

last: Roberg


title: An integrated functional and clinical genomics approach reveal genes driving aggressive metastatic prostate cancer [RNA-Seq]

first: Raunak

last: Shrestha

overall_design: RNA-seq was performed in AR knockdown, KIF4A knockdown, and WDR62 knockdown in LnCaP prostate cancer cells

first: Rajdeep

last: Das

first: Felix

last: Feng

first: Luke

middle: A

last: Gilbert


title: Expression data of HNSCC cell lines grown without and with patient-matched CAFs in 2D

summary:
Cancer associated fibroblasts (CAFs) are the major cellular component of the tumor microenvironment and they have been shown to stimulate tumor growth, epithelial-to-mesenchymal transition (EMT), invasion and radio-resistance.
We used microarrays to investigate the influence of CAFs on the gene expression profile of HNSCC cells in 2D co-cultures

overall_design: HNSCC cells (LK0824, LK0858, LK0923, LK0942, LK0949) grown as CAF co-culture in 2D were selected  for RNA extraction and hybridization on Affymetrix microarrays.

first: Matti

last: Kankainen


title: A novel class of CLK kinases inhibitors that target SRSF10 and promote p53-mediated cytotoxicity on human colorectal cancer cells

city: Toronto

first: Micheal

last: Tyers

state: Ontario

address: 555 University Avenue

institute: The Hospital for Sick Children

summary: The elevated expression of the splicing regulator SRSF10 in metastatic colorectal cancer (CRC) stimulates the production of the pro-tumorigenic Bclaf1-L splice variant. We discovered a group of small molecules with an aminothiazole carboxamide core (GPS167, GPS192 and others) that decrease production of Bclaf1-L. While additional alternative splicing events regulated by SRSF10 are affected by GPS167/192 in HCT116 cells (e.g., in MDM4, WTAP, SLK1 and CLK1), other events are shifted in a SRSF10-independent manner (e.g., in MDM2, NAB2 and TRA2A). GPS167/192 increased the interaction of SRSF10 with the CLK1 and CLK4 kinases, leading us to show that GPS167/192 are CLK kinase inhibitors preferentially impacting the activity of SRSF10. Notably, GPS167 impairs the growth of CRC cell lines and organoids, inhibits anchorage-independent colony formation, cell migration, and promotes cytoxicity that requires SRSF10 and p53. In contrast, GPS167 only minimally affects normal colonocytes and normal colorectal organoids. Thus, GPS167 reprograms the tumorigenic activity of SRSF10 in CRC cells to elicit p53-dependent apoptosis.

overall_design: Genome-wide CRISPR/Cas9 screens to test for gene deletions that affect fitness in human cells treated with CLK inhibitors KH-CB19, TG003 and GPS167.

first: Mohammad

last: Sohail

first: Lulzim

last: Shkreta

first: Johanne

last: Toutant

first: Safwat

last: Rabea

first: Jean-Philippe

last: Babeu

first: François

last: Boudreau

first: Morgane

last: Placet

first: Fernand-Pierre

last: Gendron

first: Sameh

last: Geha

first: Michael

first: David

last: Grierson

first: Benoit

last: Chabot


title: HCV poly U/UC sequences induced abnormal inflammation leads to metabolic disorders in Vulvar Lichen Sclerosis

city: Shanghai

first: Shengwei

last: Zhang

state: Shanghai

address: Songhu street

institute: Fudan University

summary: While VLS is a serious skin disease affecting women in an annoying, embarrassing, and prolonged way worldwide, its pathogenesis and molecular characteristics are still unexploreed. Previous studies have suggested the correlation between inflammation or microRNA and VLS, but the lack of comprehensive understanding on its mechanism prevents the development of precision medicine for it.  For a long time, VLS has been speculated as an autoimmune disease (Tran, Tan et al., 2019). This hypothesis was derived from several clinical observations: (1) VLS is frequently observed in women with an autoimmune diseases called Turner Syndrome (Chakhtoura, Vigoureux et al., 2014) ; (2) Many VLS patients also develop various autoimmune diseases (Kreuter, Kryvosheyeva et al., 2013, Song, Xiaoli et al., 2018) ; (3) VLS patients may also have higher frequency of certain HLA antigens, though few immunological consequence has been studied (Sideri, Rognoni et al., 1988). Microarray assay found upregulation of Th1, microRNA-155 and relative transcripts using VLS and healthy donors biopsies (Ren, Zhao et al., 2018, Terlou, Santegoets et al., 2012). However, the person-to-person genotype variation can hardly eliminate without using normal tissues from the same patient; and the PCR-based measurement of transcriptome of microarray limited the data interpretation and assumption validation.  In this article, we performed multi-omics analyses on VLS paired-samples from the same patients as well as the normal ones from healthy donors. RNA-seq analysis revealed VLS patients are suffering from abnormally high inflammation with impressive anti-virus features. In-depth analysis of their transcriptome identified a remarkable enrichment of HCV poly U/UC sequence in VLS transcriptome, which might contribute to the onset of VLS. Multi-omics results indicated various inflammation-induced metabolic disorders in VLS samples, which might serve as therapeutic targets for precision medicine.

overall_design: Examination of 4 normal donors' control samples and 18 patient donors' samples with RNA-seq.

first: Lili

last: Wang

first: Jin

last: Li


title: Malaria-parasite survival of host fever is linked to artemisinin resistance

status: Public on Jun 14 2021

city: Tampa

first: Jenna

last: Oberstaller

state: FL

address: 3720 Spectrum Blvd.

department: Genomics

institute: University of South Florida

summary: RNAseq data profiling two heatshock-sensitive P. falciparum piggyBac mutants with and without exposure to febrile temperatures.

overall_design: Each run-folder contains paired-end fastq data for two complete bioreps of the three parasite lines (NF54 wild-type control; heatshock-sensitive mutants {delta}DHC and {delta}LRR5--referred to in sample-names as PB4 and PB31, respectively) collected after 8 hours with or without exposure to febrile temperatures (41C and 37C, respectively). All parasites were at ring-stage at point of harvest as verified by Giemsa-stained microscopy. Each sample was run twice on an Illumina Miseq--the second run using total reads for each sample from the first run to inform concentration needed for each sample in run2 to ensure equal coverage of all samples.

first: Min

first: Chengqi

first: Rays

last: Jiang

first: John

last: Adams

first: Phaedra

last: Thomas

first: Thomas

last: Otto

first: Debora

last: Casandra

first: Sandhya

last: Boyapalle

first: Swamy

middle: R

last: Adapa

first: Shulin

last: Xu

first: Katrina

last: Button-Simons

first: Matthew

last: Mayho

first: Julian

middle: C

last: Rayner

middle: T

last: Ferdig


title: Immunogenicity of BRCA1-deficient Ovarian Cancers is Driven through DNA Sensing and is  Augmented by PARP Inhibition (Hi-C)

first: George

last: Coukos

overall_design: The human ovarian cancer cell line UWB1.289,which harbors a deleterious mutation in BRCA1 exon11 and LOH, was profiled its chromatin structure by HiC. Same experimental procedure was followed for UWB1.289 BRCA1 wt reconstituted isogenic pair.

first: Denarda

last: Dangaj

first: Sora

last: Chee

first: Brian

last: Stevenson

first: Julien

last: Dorier

first: Bing

last: Ren

first: Christian

last: Iseli


title: MicroRNAs  dysregulation in experimental interstitial cystitis

status: Public on Jun 12 2021

city: Memphis

first: Udai

middle: P

last: Singh

address: 881 Madison Avenue

department: Pharmacy

institute: University of Tennessee Health Science Center

summary:
We compared the chnages in urinary bladder and iliac lymph nodes microRNAs in the control and experimental autoimmune cystitis in mice.
A set of urinary bladder microRNAs (miRNAs) shows profound upregulation or downregulation in the expression profiles of the experimental IC as compared to control.

overall_design: We observed distinct miRNAs expression patterns for the EAC groups as compared to the controls, suggesting that EAC may result from the dysregulation of miRNAs in the urinary bladder and ILNs. To the best of our knowledge, this is the first report on changes in the urinary bladder and ILNs miRNAs expression in an experimental mouse model of IC.


title: RNA-sequencing explores the transcriptional profile of Wild Type and Fabp3-null mice under physiologicl and cardiac hypertrophic conditions

first: Lingfang

last: Zhuang

address: 197 Rui Jin Road II

department: Department of Vascular & Cardiology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Background: Cardiac hypertrophy was accompanied by various cardiovascular diseases (CVDs), due to the high global incidence and mortality of CVDs, it has become increasingly critical to characterize the pathogenesis of cardiac hypertrophy. We aimed to determine the metabolic effects of fatty acid binding protein 3 (FABP3), on transverse aortic constriction (TAC)-induced cardiac hypertrophy.  Methods and Results: TAC or Ang II treatment markedly upregulated Fabp3 expression. Notably, Fabp3 ablation aggravated TAC-induced cardiac hypertrophy and cardiac dysfunction. Multi-omics analysis revealed that Fabp3-deficient hearts exhibited disrupted metabolic signatures characterized by increased glycolysis, toxic lipid accumulation, and compromised fatty acid oxidation and ATP production under hypertrophic stimuli. Mechanistically, FABP3 mediated metabolic reprogramming by directly interacting with PPARα, which prevented its degradation and synergistically modulated its transcriptional activity on Mlycd, Gck. Finally, treatment with the PPARα agonist, fenofibrate, rescued the pro-hypertrophic effects of Fabp3 deficiency.

overall_design: Cardiac mRNA from sham or transverse aortic constriction (TAC)-operated WT and Fabp3-null mice were collected for RNA-sequencing analysis, and three independent biological replicates were included in this study.

first: Zizhu

last: Liu

first: Chenni

last: Li

first: Qi

last: Jin

first: Lin

last: Lu

first: Rong

last: Tao

first: Xiaoxiang

last: Yan

first: Kang

last: Chen


title: Mild food restriction and gene expression profile (muscle)

status: Public on Jun 08 2021

city: bunkyo-ku

first: Kenji

last: Saito

department: Department of Applied Biological Chemistry

institute: The Univeristy of Tokyo

summary: The aim of this study is to obtain the gene expression profiles of the muscle of young growing rats after mild restriction of food intake for one week or one month.

overall_design: Male Wistar rats, at 6 weeks of age, were fed with reduced diet (5%, 10%, 20% and 30% restriction) for one week or one month (n=5). After 16h fasting, the muscle was then extracted and total RNA was isolated using an RNeasy mini kit with DNase treatment (QIAGEN). The RNA samples were pooled from five rats for each group. Then, DNA microarray analysis was performed using the GeneChip (Affymetrix) on each pooled RNA sample.

first: K

first: H

last: Kato


title: Mild food restriction and gene expression profile (intestine)

summary: The aim of this study is to obtain the gene expression profiles of the intestine of young growing rats after mild restriction of food intake for one month.

overall_design: Male Wistar rats, at 6 weeks of age, were fed with reduced diet (5%, 10%, 20% and 30% restriction) for one month (n=5). After 16h fasting, the small intestine was then extracted and total RNA was isolated using an RNeasy mini kit with DNase treatment (QIAGEN). The RNA samples were pooled from five rats for each group. Then, DNA microarray analysis was performed using the GeneChip (Affymetrix) on each pooled RNA sample.


title: Dynamic landscape of protein occupancy across the Escherichia coli chromosome

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

summary: In bacteria, adaptive regulation of gene expression occurs through the precise interactions of hundreds of DNA binding proteins across the chromosome. Decades of research has revealed the identity and functions of many of these regulators. However, a systems-level understanding of gene expression requires simultaneous, comprehensive monitoring of these interactions as a function of genetic and environmental perturbations. Here we present a high-resolution in vivo protein occupancy display (IPOD-HR) technology that enables quantitative and comprehensive monitoring of DNA-protein interactions across a bacterial chromosome. The global nature of IPOD-HR permits simultaneous activity profiling of all known sequence specific transcription factors and discovery of novel condition-dependent DNA-binding proteins. We show that global IPOD-HR profiles can be used for de novo discovery of sequence specificity motifs for active transcription factors. IPOD-HR also reveals many large domains of extended protein occupancy that define relatively stable, transcriptionally silent regions with unique sequence and gene functional features. IPOD-HR thus provides a unique form of systems-level access to transcriptional regulatory states that will allow rapid profiling and characterization of both known and novel regulatory logic in bacteria. We provide here IPOD-HR occupancy results across a range of genetic and physiological perturbations, as detailed in the accompanying manuscript.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: IPOD, Input, and RNA polymerase ChIP data (2 or more replicates each) for cells from each of seven different conditions

first: Peter

middle: L

first: Haley

last: Amemiya

first: Thomas

last: Goss

first: Saeed

last: Tavazoie


title: ChIP-seq analysis of H3K4me3, H3K27ac and H3K27me3 in the neural stem/progenitor cells under crotonate treatment

city: beijing

first: Peipei

last: liu

address: No. 25-1 West Beisihuan Rd, Haidian District, Beijing

department: State Key Laboratory of Stem cells and Reproductive Biology

institute: institute of zoology,Chinese academy of sciences

summary: To gain a deeper insight into how crotonate regulates embryonic neural stem/progenitor cells (NSPCs) proliferation and differentiation, ChIP-seq was performed to analyze the genome-wide changes of H3K4me3, H3K27ac and H3K27me3 stimulated with crotonate in E13.5 NSPCs.

overall_design: ChIP-seq was performed before and after crotonate treatment, and sequenced on Illumina NovaSeq 6000 platform.

first: Shang-Kun

last: Dai


title: Mild food restriction and gene expression profile

overall_design: Refer to individual Series


title: Mild food restriction and gene expression profile (adipose)

summary: The aim of this study is to obtain the gene expression profiles of the adipose tissue of young growing rats after mild restriction of food intake for one week or one month.

overall_design: Male Wistar rats, at 6 weeks of age, were fed with reduced diet (5%, 10%, 20% and 30% restriction) for one week or one month (n=5). After 16h fasting, the adipose tissue was then extracted and total RNA was isolated using an RNeasy mini kit with DNase treatment (QIAGEN). The RNA samples were pooled from five rats for each group. Then, DNA microarray analysis was performed using duplicate GeneChips (Affymetrix) on each pooled RNA sample.


title: Comparison of extracellular vesicle and filamentous cell transcriptomes of Ustilago maydis

city: Düsseldorf

first: Michael

last: Feldbrügge

address: Universtitätstr. 1

department: Biology

institute: Heinrich-Heine University Düsseldorf

summary: The coding transcriptomes of filamentous cultures of the maize smut fungus Ustilago maydis and their extracellular vesicles (EVs) were compared. Protein-coding transcripts relatively enriched in EVs versus filament cells were identified and examined to identify potentially functional mRNA cargos of U. maydis EVs.

overall_design: Poly(A)-enriched libraries were generated from four biological replicates each of Mock- (PBS) and RNase-treated extracellular vesicle preparations and the corresponding filamentous cells (4 biological replicates x 3 samples each). Sequencing was carried out on Illumina MiSeq platform with v3 chemistry (2x 150 bp paired-end sequencing).

first: Seomun

last: Kwon

first: Andreas

last: Brachmann

first: Oliver

last: Rupp


title: ZBTB32 performs crosstalk with the glucocorticoid receptor and is crucial in glucocorticoid responses to starvation

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: The hypothalamic-pituitary-adrenal (HPA) axis forms a complex neuroendocrine system that interacts directly via feedforward and feedback reactions to regulate the body’s response to stress such as starvation. In contrast with the glucocorticoid receptor (GR), ZBTB32 (zinc finger and BTB domain containing 32) is a transcription factor with very poorly described functional relevance in physiology. We investigated the importance of ZBTB32 on the HPA axis functioning and found that it is essential for the production of glucocorticoids (GCs) in response to starvation, because ZBTB32-/- mice fail to increase the GC production during prolonged absence of nutrients. In terms of mechanism, GR-mediated upregulation of adrenal Scarb1 gene expression was absent in ZBTB32-/- mice, implicating defective cholesterol import as the cause of the poor GC synthesis. Lower GC levels in ZBTB32-/- mice are further associated with aberrations in the metabolic adaptation to starvation, which could potentially explain the progressive weight gain of ZBTB32-/- mice. Moreover, this study identifies that ZBTB32 performs a crosstalk with the GR in the metabolic adaptation to starvation via regulation of adrenal GC production.

overall_design: Genome wide expression profiling of response to DEX (2h) in wild type and Zbtb32 KO mice. A total of 4 conditions (3 biological replicates per condition) were used in total

first: Lise

last: Van Wyngene

first: Tineke

last: Vanderhaeghen

first: Ioanna

last: Petta

first: Katrien

last: Corbeels

first: Bart

last: Van der Schueren

first: Jolien

last: Vandewalle

first: Kelly

last: Van Looveren

first: Charlotte

last: Wallaeys

first: Melanie

last: Eggermont

first: Sylviane

last: Dewaele

first: Leen

last: Catrysse

first: Geert

last: Van Loo

first: Rudi

last: Beyaert

first: Roman

last: Vangoitsenhoven

first: Toshinori

last: Nakayama

first: Jan

last: Tavernier

first: Karolien

last: De Bosscher

first: Claude

last: Libert


title: Mild food restriction and gene expression profile (brain)

first: Kenji

last: Saito

summary: The aim of this study is to obtain the gene expression profiles of the brain of young growing rats after mild restriction of food intake for one week or one month.

overall_design: Male Wistar rats, at 6 weeks of age, were fed with reduced diet (5%, 10%, 20% and 30% restriction) for one week or one month (n=5). After 16h fasting, the brain was then extracted and total RNA was isolated using an RNeasy mini kit with DNase treatment (QIAGEN). The RNA samples were pooled from five rats for each group. Then, DNA microarray analysis was performed using the GeneChip (Affymetrix) on each pooled RNA sample.

first: K

first: H

last: Kato


title: High Shear Stress Enhances Endothelial Permeability in the presence of a CAD Risk Locus

city: La Jolla

first: Adam

middle: Jeffrey

last: Engler

state: CA

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: UC San Diego

summary: Single nucleotide polymorphisms are exceedingly common in non-coding loci, yet their impact on cellular dysfunction–especially under stressed conditions associated with coronary artery disease (CAD)–is still unclear. Here we show that when exposed to external stressors, the presence of polymorphisms in the non-coding 9p21.3 locus increases endothelial monolayer and microvessel dysfunction; endothelial cells (ECs) derived from induced pluripotent stem cells of patients homozygous for this risk haplotype (R/R WT) differentiated similarly to their non-risk (N/N) and isogenic knockout (R/R KO) counterparts; monolayers exhibited greater permeability and ROS signaling when the risk locus was present. Addition of the inflammatory cytokine TNFa further enhanced EC monolayer permeability but independent of risk haplotype. When wall shear stress was applied to ECs in a microfluidic vessel, R/R WT vessels were more permeable at lower shear stresses than R/R KO vessels. Transcriptomes of sheared cells clustered more by risk haplotype than by patient or clone, resulting in significant differential regulation of EC function and junction genes versus static conditions. A subset of previously identified CAD risk genes invert expression patterns in the presence of high shear concomitant with aberrant cell-cell adhesion, vessel permeability, and the risk haplotype, suggesting that shear stress could be a unique regulator of non-coding loci and its impact on CAD.

overall_design: RNA-sequencing profiles of iPSC-derived endothelial cells under static, shear, and TNFalpha conditions

first: Evan

last: Teng

last: Masutani


title: Gene expression profiling during RANKL-mediated osteoclast differentiation

city: Seoul

first: Myoung Jun

last: Kim

address: 120 Neungdong-ro, Gwangjin-gu

institute: konkuk university

summary:
The hexosamine biosynthetic pathway (HBP) is a pathway that requires glucose using approximately 3% ~ 5% of total glucose coming into cells. HBP synthesizes UDP-GlcNAc using not only glucose but also various metabolic products such as those amino acid, fatty acid and nucleotide. O-GlcNAcylation by Ogt is considered the act as a nutrient sensor because the amount of UDP-GlcNAc is influenced by various metabolites. Therefore, when the balance of O-glcnacylation is broken, it induces diseases such as cancer or neurological diseases or affects the differentiation of cells.
 Bone homeostasis is regulated by osteoblasts that produce bone and osteoclasts that resorb bone. Disruption of this balance leads to diseases such as osteoporosis. Previous studies reported that osteoblast differentiation was inhibited by excessive O-GlcNAcylation. Increased o-glcnacylation of runx2 induced bone homeostasis imbalance by reducing the transcriptional activity of runx2 and mRNA expression of the target gene of runx2 involved in osteoblast differentiation. However, how O-GlcNAcylation regulates differentiation of osteoclast remains unclear. So, the goals of our study are to describe expression changes in genes expression associated with O-GlcNAcylation during RNAKL-mediated osteoclast differentiation.

overall_design:
Transcriptome analysis of osteoclastogenesis
BMMs were treated with 30 ng/ml M-CSF and 100 ng/ml RANKL for 0, 24, 48, 72 hours.

first: Jueng

middle: S

last: You

first: Hyuk

first: Myoung


title: RNA degradation is required for the germ cell-to-maternal transition in Drosophila

city: Albany

first: Patrick

last: Blatt

address: 1400 Washington Ave

institute: SUNY Albany

summary: In sexually reproducing animals, the oocyte contributes a large supply of RNAs that are essential to launch development upon fertilization. The mechanisms that regulate the composition of the maternal RNA contribution during oogenesis are unclear. Here, we show that a subset of RNAs expressed during the early stages of oogenesis is subjected to regulated degradation during oocyte specification. Failure to remove these RNAs results in oocyte dysfunction and death. We identify the RNA-degrading Super Killer complex and No-Go Decay factor Pelota as key regulators of oogenesis via targeted degradation of specific RNAs expressed in undifferentiated germ cells. These regulators target RNAs enriched for cytidine sequences that are bound by the polypyrimidine tract binding protein Half pint. Thus, RNA degradation helps orchestrate a germ cell-to-maternal transition by sculpting RNAs that become part of the maternal contribution to the zygote.

overall_design: RNA-seq of mRNA and polysome associated mRNA for various mutant conditions

first: Siu-Wah

last: Wong-Deyrup

first: Alicia

last: McCarthy

first: Shane

last: Breznak

first: Matthew

middle: D

last: Hurton

first: Maitreyi

last: Upadhyay

first: Benjamin

last: Bennink

first: Justin

last: Camacho

first: Miler

last: Lee

first: Prashanth

last: Rangan


title: Tumor Microenvironment-induced BRD4 Activation Results in Chromatin Remodeling and Therapy Resistance in Colorectal Cancer

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore

summary: Analysis of gene expression profiles of patient-derived colorectal cancer cell which is mono-cultured or co-cultured with CAFs in the presence of vehicle, JQ1, pacritinib or combo.

first: Wenyu

last: Wang

last: Oguz

first: Qiang

last: Yu


title: Nuclear receptor NHR-49 promotes peroxisome proliferation to compensate for aldehyde dehydrogenase deficiency in C. elegans

status: Public on Jun 07 2021

city: Hong Kong

first: Ho Yi

last: Mak

address: Clear Water Bay

department: Division of Life Science

institute: The Hong Kong University of Science and Technology

summary: The intracellular level of fatty aldehydes is tightly regulated to minimize the formation of toxic aldehyde adducts of cellular components. Accordingly, deficiency of a fatty aldehyde dehydrogenase FALDH causes the neurologic disorder Sjögren-Larsson syndrome (SLS) in humans. However, cellular responses to unresolved, elevated fatty aldehyde levels are poorly understood. Based on lipidomic and imaging analysis, we report that the loss of endoplasmic reticulum-, mitochondria- and peroxisomes-associated ALH-4, the C. elegans FALDH ortholog, increases fatty aldehyde levels and reduces fat storage. ALH-4 deficiency in the intestine, cell-nonautonomously induces NHR-49/NHR-79-dependent hypodermal peroxisome proliferation. This is accompanied by the upregulation of catalases and fatty acid catabolic enzymes, as indicated by RNA sequencing. Such a response is required to counteract ALH-4 deficiency since alh-4; nhr-49 double mutant animals are not viable. Our work reveals unexpected inter-tissue communication of fatty aldehyde levels, and suggests pharmacological modulation of peroxisome proliferation as a therapeutic strategy for SLS.

overall_design: RNA-seq with three biological replicates of synchronized wild type N2 and mutant alh-4(-) worms at the L4 stage to determine the differentially expressed genes.

first: Lidan

last: Zeng

first: Christopher

middle: B

last: Preusch

first: Gary

last: He

first: Tom

last: Cheung

first: Ho


title: Next generation sequencing transcriptome analysis of patient-derived macrophages stimulated with SARS-CoV-2 protein

city: Cologne

first: Alexander

last: Simonis

address: Kerpener Str. 62

institute: University Hospital of Cologne

summary: Innate immunity triggers responsible for viral control or hyperinflammation in COVID-19 are largely unknown. Here we show that the SARS-CoV-2 spike protein (S-protein) primes inflammasome formation and release of mature interleukin-1β (IL-1β) in macrophages derived from COVID-19 patients but not in macrophages from healthy SARS-CoV-2 naïve individuals. Furthermore, longitudinal analyses reveal robust S-protein driven inflammasome activation in macrophages isolated from convalescent COVID-19 patients, which correlates with distinct epigenetic and gene-expression signatures suggesting innate immune memory after recovery from COVID-19. Importantly, we show that S-protein driven IL-1β secretion from patient-derived macrophages requires non-specific monocyte pre-activation in vivo to trigger NLRP3-inflammasome signaling. Our findings reveal that SARS-CoV-2 infection causes profound and long-lived re-programming of macrophages resulting in augmented immunogenicity of the SARS-CoV-2 S-protein, a major vaccine antigen and potent driver of adaptive and innate immune signaling.

overall_design: RNA profiles of patient-derived macrophages from SARS-CoV-2 convalescent patients and SARS-CoV-2 naïve individuals stimulated with SARS-CoV-2 spike protein, lipopolysaccharide or without stimulation.

first: Sebastian

last: Theobald

first: Theodoros

last: Georgomanolis

first: Jan

last: Rybniker


title: Topological isolation as a mechanism for precise control of developmental regulators in mammalian genomes (Hi-C II)

status: Public on Jun 06 2021

city: Beijing

first: Hua-Jun

last: Wu

state: Beijing

address: 8 science park road, zhongguancun life science park

department: School of Basic Medical Sciences

institute: Peking University Health Science Center

summary: Recent investigation of insulated chromosome structures suggests their crucial role in controlling proper gene expression. However, it remains unclear whether developmental regulators can be precisely controlled by such insulated structures and whether developmental failure is caused by disrupting the structure boundaries. Here we identified topologically insulated regions (TIRs) from deeply sequenced human embryonic stem cell (hESC) Hi-C data and analyzed the gene distribution across TIRs. We find a notable enrichment of developmental regulators isolated from other genes by TIRs and show that the boundary CTCF sites are highly conserved across species. Perturbation of such boundaries in hESCs leads to failure to properly differentiate. Enhancer activity is restricted by such boundaries, further pointing towards their regulatory importance. Finally, germline mutations affecting such boundaries are subject to purifying selection and are underrepresented in the human population. Our findings provide new insights into mammalian genome organization and suggest a possible role of gene insulation through chromosomal folding structures for precise control of developmental regulators.

overall_design: Capture HiC-Seq of SOX17 upstream CTCF wildtype and knockout in embryonic differentiation

first: Alexandro

last: Landshammer

last: Meissner

first: Franziska

last: Michor


title: Topological isolation as a mechanism for precise control of developmental regulators in mammalian genomes [RNA-seq II]

overall_design: RNA-Seq of rescue experiment on SOX17 upstream CTCF knockout in embryonic differentiation


title: Topological isolation as a mechanism for precise control of developmental regulators in mammalian genomes [4C-seq]

overall_design: 4C-Seq of SOX17 upstream CTCF wildtype and knockout in embryonic differentiation


title: Genome-wide mapping of H3K4me3 and H3K27ac in monocytes from SARS-CoV-2 convalescent patients.

summary: Epigenetic alterations of monocytes from COVID-19 convalescent individuals and healthy controls have been analyzed by mapping trimethylated H3K4 (H3K4me3) and acetylated H3K27 (H3K27ac) genome-wide using CUT&RUN (Skene & Henikoff, 2017). Epigenetic reprogramming of myeloid cells represents a hallmark of trained innate immunity (Netea, Joosten et al., 2016). In general, active enhancers are marked by H3K27ac and transcription start sites are marked by H3K4me3 and H3K27ac (Kimura, 2013). A global analysis of histone modifications associated with transcription start sites (TSS) revealed a difference in the overall coverage of specific loci in SC-conv versus SC-naïve cells with SC-conv samples showing lower occupancy overall

overall_design: Monocytes were isolated from COVID-19 convalescent (n = 4 ) and healthy individuals (n = 4) for this study.


title: Tumor Microenvironment-induced BRD4 Activation Results in Chromatin Remodeling and Therapy Resistance in Colorectal Cancer [ChIP-seq]

last: OGUZ

summary: Tumor microenvironment promotes tumorigenesis, but its role in modulating tumor chromatin activity is poorly understood. Here, we show that inflammatory cytokines interleukin-6 and -8 in the tumor microenvironment induces JAK2-mediated phosphorylation of bromodomain-containing protein 4 (BRD4), which results in interaction with UCHL3 deubiquitinase, leading to increased BRD4 protein stabilization in colorectal cancer. JAK2-phosphorylated BRD4 shows enhanced activity binding to chromatin but reduced binding to BRD4 inhibitors, leading to treatment resistance. Moreover, BRD4 phosphorylation promotes interaction with STAT3 to induce chromatin remodeling through concurrent binding to enhancers and super-enhancers, supporting a tumor-promoting transcriptional program. Thus, the inflammatory tumor microenvironment provides a powerful mechanism for tumor chromatin remodeling and oncogenic transcription, which suggests a unrecognized new strategy to enhance BRD4 inhibitor response.

overall_design: Examination of 4 differents transcription/epigenetic regulators in patient-derived colorectal cancer cells with/without IL6/8 treatment.


title: Electrophysiological defects in a novel patient-derived stem cell model of desmoglein-2 mutant ARVC

city: Baltimore

first: Suraj

last: Kannan

address: 720 Rutland Avenue Ross 954

department: Cardiology

institute: Johns Hopkins University

summary: Here we developed a novel human induced pluripotent stem cell (hiPSC) model of ARVC to gain insight into the electrical and biomolecular effects of desmoglein-2 (DSG2) mutation in cardiomyocytes. hiPSC-derived cardiomyocytes (hiPSC-CMs) were generated from peripheral blood mononuclear cells donated by an ARVC patient with a pathogenic variant in DSG2, c.2358delA.

overall_design: DSG2Mut hiPSC-CMs were compared against a control line via bulk RNA-seq.

first: Robert

middle: N

last: Hawthorne

first: Adriana

last: Blazeski

first: Justin

last: Lowenthal

first: Roald

last: Teuben

first: Deborah

last: DiSilvestre

first: Jeffrey

middle: E

last: Saffitz

first: Cynthia

last: James

first: Kenneth

last: Boheler

first: Stephen

last: Chelko

first: Gordon

last: Tomaselli

first: Leslie

last: Tung